Tuning the Growth and Mechanical Properties of Calcite Using Impurities: Insight from Molecular Simulation

Over many millions of years, evolution has provided living organisms with the tools to control the growth and properties of materials from the molecular scale upward. One of the many ways this is achieved is through the introduction of impurities into the solution in which these materials grow. A long-term goal of materials scientists is to harness nature's control mechanisms and apply them in the world of engineering. However, these mechanisms of growth control are highly complex, and understanding them requires insight into physical processes at the molecular scale. While experiments are so-far unable to offer such a high resolution, computer simulations can be used to directly model these physical process with no limit on the resolution. Throughout this thesis, an array of computational methodologies is applied to calcite in an attempt to understand how impurities are able to drive the growth process, and ultimately alter the mechanical properties of the crystal. A series of metadynamics simulations are applied to calcite kink sites, revealing a more complex growth mechanism in which kink-terminating ions do not initially occupy their crystal lattice sites, and only do so upon the adsorption of an additional solute. A combination of metadynamics and Kinetic Monte Carlo simulations are used to examine the adsorption free energies and growth inhibiting properties of amino acids and polyamines, the results of which are compared directly to experiment. This offers a robust insight into the molecular mechanisms that underpin how organic molecules are able to tune the growth of calcite. Simulations are also applied to two case studies of impure calcite. By examining lattice spacings, determining stress distributions and simulating a series of crack propagation events, insight into mechanisms through which biogenic crystals exhibit superior mechanical properties is found. Finally, the nature of non-Markovianity when using reaction coordinates -such as those used in rare event methodologies applied throughout this thesis- are investigated. By introducing non-Markovianity into the system, barrier crossing rates in a coarse-grained system more closely resemble those in the original two-dimensional system. Furthermore, we study the breakdown in rare-events sampling when a poor reaction coordinate is used, and identify which rare-events sampling techniques are more appropriate for detecting poor reaction coordinate choices

Nonequilibrium capture of impurities that completely block kinks during crystal growth

Some impurities cannot integrate into isolated kinks because they completely block the growth of the kinks to which they adsorb. For this class of impurity, we derive an equation for the amount that incorporates into a crystal during growth of the elementary step by assuming that such an impurity incorporates if and only if it gets captured between a kink and an antikink. We show that the impurity concentration in the crystal increases monotonically with the impurity concentration in the mother phase, but that it can vary non-monotonically with both the supersaturation of the mother phase and the kink density of the step. In contrast to other capture mechanisms, we find that weakly adsorbed impurities incorporate to an extent that is independent of the supersaturation when the supersaturation is high. Irrespective of the growth conditions, the amount of impurity that can incorporate into a crystal is limited by an upper bound determined by the kink density

Calcite Kinks Grow via a Multistep Mechanism

The classical model of crystal growth assumes that kinks grow via a sequence of independent adsorption events where each solute transitions from the solution directly to the crystal lattice site. Here, we challenge this view by showing that some calcite kinks grow via a multistep mechanism where the solute adsorbs to an intermediate site and only transitions to the lattice site upon the adsorption of a second solute. We compute the free energy curves for Ca and CO3 ions adsorbing to a large selection of kink types, and we identify kinks terminated both by Ca ions and by CO3 ions that grow in this multistep way